Generating Bond Distances and Bond Angles

You may have to play with the limits to get the coverage of bonds that you are interested. The following DLS template restraints will obtain the intramolecular distances and angles (the following no spaces between the # and command):

#rele punch dls.txt
#DISTANCE
OUTPUT PUNCH=RESTRAIN
end

#rele punch dummy.txt           (Releases and unlocks the previous dls.txt file from Crystals)

Some other options for Generating Bond Distances and Bond Angles

You may have to play with the limits to get the coverage of bonds that you are interested. Following is an example of playing with the LIMITS option which would also generate retraints to ajacent molecules:

#rele punch dls2.txt
#DISTANCE
OUTPUT PUNCH=RESTRAIN
SELECT TYPE=INTRA RANGE=LIMITS  (supresses bonds and angles to atoms in nearby symmetry
                                 generated molecules)
LIM 0 4 0 0                     (set the limits in Angstrom on how far the bonds and angles should search.
                                    LIMITS DMINIMUM= DMAXIMUM= AMINIMUM= AMAXIMUM= )  
end

#rele punch dummy.txt           (Releases and unlocks the previous dls.txt file from Crystals)

Edit the dls.txt (or whatever you have called this file) and change the distances/angle restraint with whatever ESD you consider appropriate to what you wish to use. The default ESD's for bond lengths are 0.01 Angstrom and for bond angles 1 degree. You may have to play with the restraint ESDs to get the desired level of flexibility.

Also fix the origin and use limits to stop the refinement sending the co-ordinates to outer-space. Thus edit the dls.txt file in your favourite text editor and add:

orig x
orig y
orig z
limit 0.01 x
limit 0.01 y
limit 0.01 z

The file might now looking something like this:

#
# Punched on 10/03/00 at 01:05:41
#
#LIST     16                                                                    
orig x
orig y
orig z
limit 0.01 x
limit 0.01 y
limit 0.01 z
DIST   1.880,.05= C(1) to S(2)
DIST   1.540,.05= C(1) to C(10)
ANGL  96,10= S(2) to C(1) to C(10)
DIST   1.880,.05= S(2) to C(3)
ANGL 109,10= C(1) to S(2) to C(3)
DIST   1.540,.05= C(3) to C(4)
ANGL 106,10= S(2) to C(3) to C(4)
DIST   1.540,.05= C(4) to N(5)
DIST   1.540,.05= C(4) to C(8)
ANGL 121,10= C(3) to C(4) to N(5)
ANGL 121,10= C(3) to C(4) to C(8)
ANGL 118,10= N(5) to C(4) to C(8)
DIST   1.540,.05= N(5) to C(6)
ANGL  99,10= C(4) to N(5) to C(6)
DIST   1.540,.05= C(6) to N(7)
ANGL 111,10= N(5) to C(6) to N(7)
DIST   1.540,.05= N(7) to C(8)
ANGL 117,10= C(6) to N(7) to C(8)
DIST   1.540,.05= C(8) to C(9)
ANGL  95,10= C(4) to C(8) to N(7)
ANGL 140,10= C(4) to C(8) to C(9)
ANGL 125,10= N(7) to C(8) to C(9)
DIST   1.540,.05= C(10) to N(11)
ANGL  96,10= C(1) to C(10) to N(11)
DIST   1.540,.05= N(11) to C(12)
ANGL 115,10= C(10) to N(11) to C(12)
DIST   1.540,.05= C(12) to N(13)
DIST   1.540,.05= C(12) to N(16)
ANGL 108,10= N(11) to C(12) to N(13)
ANGL 134,10= N(11) to C(12) to N(16)
ANGL 117,10= N(13) to C(12) to N(16)
DIST   1.540,.05= N(13) to C(14)
ANGL 126,10= C(12) to N(13) to C(14)
DIST   1.540,.05= C(14) to N(15)
ANGL 174,10= N(13) to C(14) to N(15)
DIST   1.540,.05= N(16) to C(17)
ANGL 125,10= C(12) to N(16) to C(17)
# Remove space after hash to activate next line
# USE LAST

#use dls.txt
end

Performing DLS refinement: telling Crystals that you do not want to refine on HKLs

In the latest GUI version of Crystals, you can use the Refinement, F or F2 and advanced options GUI to instruct Crystals not to use reflections. Just declick the Use Reflections checkbox but make sure the Use Restraints checkbox is "on".

You can also use the following command line method to tell Crystals that you "do not want" to refine on any HKLs (answer the questions this script queries you on).

#script inlist23

When prompted with:

Do you wish to use LIST 6 reflections? (keyword [YES])

Type NO

From David Watkin: "But since crystals has no way of predicting what distortion of the structure you would like to try, you have to modify them by hand. HOWEVER, all the symmetry related bonds and angles are listed, and since this technique is usually used for high symmetry materials, this is a great saving. In addition to the distance and angle restraints, you can also add in any/all of the other features. Its a great way for saying 'what if?' and trying a new SG or something."

Crystals is instructed to refine the atomic positions of the restrained atoms using the following:

#list 12
block x's
end

To refine, use either from the script command line:

\SFLS
REFINE
END

Zero Cycles of DLS Refinement

First Cycle of DLS Refinement

Converged

To go back one refinement step you can refer to Multiple UNDO in Crystals - restoring old structure models in Crystals or use:

#disk
reset 5 0 -1
end

This demonstration continues on with Setting up Planar Restraints in Crystals

and with

Setting up and Refining on a Rigid Body (5 membered ring) in Crystals